Rdbi.PgSQL segmentation faults
0
0
Entering edit mode
Ido M. Tamir ▴ 320
@ido-m-tamir-1268
Last seen 10.2 years ago
Hi, since trying to load my data with Rdbi.PgSQL I am getting segmentation faults as soon as I try to access my returned dataframes. getAll <- function(){ key <- read.sampleKey() con <- dbConnect(PgSQL(),host = "localhost", dbname = "test") result <- dbSendQuery( con, paste("SELECT * FROM all" )) val <- dbGetResult( result ) dbClearResult(result) dbDisconnect(con) return(val) } as soon as I call this function and then print(val) or source the file again I get someting like the error dumps below or Segmentation faults. Thank you very much for answers, tips (switch to mysql?) etc... ido System: fedora core 4: postgresql-8.0.3-1 postgresql-libs-8.0.3-1 postgresql-server-8.0.3-1 postgresql-tcl-8.0.3-1 postgresql-contrib-8.0.3-1 postgresql-jdbc-8.0.3-1 postgresql-pl-8.0.3-1 postgresql-python-8.0.3-1 postgresql-docs-8.0.3-1 postgresql-devel-8.0.3-1 postgresql-odbc-08.00.0100-1 postgresql-test-8.0.3-1 R: Version 2.1.1 Rdbi "Rdbi" "/usr/lib/R/library" "1.1.2" NA RdbiPgSQL "RdbiPgSQL" "/usr/lib/R/library" "1.1.4" NA *** glibc detected *** /usr/lib/R/bin/exec/R: double free or corruption (!prev): 0x097c43e0 *** ======= Backtrace: ========= /lib/libc.so.6[0x174424] /lib/libc.so.6(__libc_free+0x77)[0x17495f] /usr/lib/libpq.so.4(PQclear+0x47)[0xa63c90] /usr/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLclearResult+0x25) [0xb24d21] /usr/lib/R/lib/libR.so(R_RunWeakRefFinalizer+0x149)[0x33fbf0] /usr/lib/R/lib/libR.so[0x33fd45] /usr/lib/R/lib/libR.so[0x341c5e] /usr/lib/R/lib/libR.so(Rf_cons+0x115)[0x3424be] /usr/lib/R/lib/libR.so(Rf_allocList+0x41)[0x342548] /usr/lib/R/lib/libR.so(Rf_matchArgs+0x43a)[0x33eda1] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x7a)[0x325219] /usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468] /usr/lib/R/lib/libR.so[0x34aed5] /usr/lib/R/lib/libR.so(Rf_usemethod+0x44e)[0x34b5b8] /usr/lib/R/lib/libR.so(do_usemethod+0x21d)[0x34bc1a] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468] /usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365] /usr/lib/R/lib/libR.so[0x323a77] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(do_for+0x224)[0x3247b8] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468] /usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365] /usr/lib/R/lib/libR.so(Rf_eval+0x411)[0x322267] /usr/lib/R/lib/libR.so[0x34abd5] /usr/lib/R/lib/libR.so(do_usemethod+0x195)[0x34bb92] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468] /usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365] /usr/lib/R/lib/libR.so(Rf_eval+0x411)[0x322267] /usr/lib/R/lib/libR.so[0x34abd5] /usr/lib/R/lib/libR.so(do_usemethod+0x195)[0x34bb92] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468] /usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(do_if+0x8d)[0x324b1b] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(do_if+0x8d)[0x324b1b] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468] /usr/lib/R/lib/libR.so[0x34aed5] /usr/lib/R/lib/libR.so(Rf_usemethod+0x44e)[0x34b5b8] /usr/lib/R/lib/libR.so(do_usemethod+0x21d)[0x34bc1a] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468] /usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468] /usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365] /usr/lib/R/lib/libR.so(do_set+0xce)[0x323fdf] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce] ======= Memory map: ======== 00111000-00235000 r-xp 00000000 03:06 65279 /lib/libc-2.3.5.so 00235000-00237000 r-xp 00124000 03:06 65279 /lib/libc-2.3.5.so 00237000-00239000 rwxp 00126000 03:06 65279 /lib/libc-2.3.5.so 00239000-0023b000 rwxp 00239000 00:00 0 0023b000-0025d000 r-xp 00000000 03:06 65317 /lib/libm-2.3.5.so 0025d000-0025e000 r-xp 00021000 03:06 65317 /lib/libm-2.3.5.so 0025e000-0025f000 rwxp 00022000 03:06 65317 /lib/libm-2.3.5.so 0025f000-00261000 r-xp 00000000 03:06 65337 /lib/libdl-2.3.5.so 00261000-00262000 r-xp 00001000 03:06 65337 /lib/libdl-2.3.5.so 00262000-00263000 rwxp 00002000 03:06 65337 /lib/libdl-2.3.5.so 00263000-00272000 r-xp 00000000 03:06 65989 /lib/libresolv-2.3.5.so 00272000-00273000 r-xp 0000e000 03:06 65989 /lib/libresolv-2.3.5.so 00273000-00274000 rwxp 0000f000 03:06 65989 /lib/libresolv-2.3.5.so 00274000-00276000 rwxp 00274000 00:00 0 00277000-00291000 r-xp 00000000 03:06 65277 /lib/ld-2.3.5.so 00291000-00292000 r-xp 00019000 03:06 65277 /lib/ld-2.3.5.so 00292000-00293000 rAborted ###################################################################### ########or: *** glibc detected *** /usr/lib/R/bin/exec/R: free(): invalid pointer: 0x00900001 *** ======= Backtrace: ========= /lib/libc.so.6[0x2f8424] /lib/libc.so.6(__libc_free+0x77)[0x2f895f] /usr/lib/libpq.so.4(PQclear+0x29)[0x437c72] /usr/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLclearResult+0x25) [0x559d21] /usr/lib/R/lib/libR.so(R_RunWeakRefFinalizer+0x149)[0x795bf0] /usr/lib/R/lib/libR.so[0x795d45] /usr/lib/R/lib/libR.so[0x797c5e] /usr/lib/R/lib/libR.so(Rf_cons+0x115)[0x7984be] /usr/lib/R/lib/libR.so(Rf_duplicate+0x23b)[0x76124b] /usr/lib/R/lib/libR.so(do_subset2_dflt+0x38d)[0x8152db] /usr/lib/R/lib/libR.so(do_subset2+0x7e)[0x815744] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464] /usr/lib/R/lib/libR.so(Rf_DispatchOrEval+0x5f)[0x77942d] /usr/lib/R/lib/libR.so(do_subset2+0x55)[0x81571b] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464] /usr/lib/R/lib/libR.so(do_set+0xce)[0x779fdf] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x77a1ce] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464] /usr/lib/R/lib/libR.so(do_if+0x47)[0x77aad5] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x77a1ce] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464] /usr/lib/R/lib/libR.so(do_for+0x224)[0x77a7b8] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464] /usr/lib/R/lib/libR.so(do_begin+0x37)[0x77a1ce] /usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x77b468] /usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x778365] /usr/lib/R/lib/libR.so(Rf_ReplIteration+0x143)[0x79303c] /usr/lib/R/lib/libR.so[0x793277] /usr/lib/R/lib/libR.so(run_Rmainloop+0x60)[0x79355b] /usr/lib/R/lib/libR.so(Rf_mainloop+0x1c)[0x794290] /usr/lib/R/bin/exec/R(main+0x23)[0x804860b] /lib/libc.so.6(__libc_start_main+0xc6)[0x2a9de6] /usr/lib/R/bin/exec/R[0x8048565] ======= Memory map: ======== 00111000-00112000 r-xp 00000000 03:06 1952785 /usr/lib/gconv/ISO8859-1.so 00112000-00114000 rwxp 00000000 03:06 1952785 /usr/lib/gconv/ISO8859-1.so 00114000-00149000 r-xp 00000000 03:06 3782777 /usr/lib/R/library/stats/libs/stats.so 00149000-0014b000 rwxp 00034000 03:06 3782777 /usr/lib/R/library/stats/libs/stats.so 0014b000-00161000 r-xp 00000000 03:06 3783664 /usr/lib/R/modules/R_X11.so 00161000-00162000 rwxp 00016000 03:06 3783664 /usr/lib/R/modules/R_X11.so 00162000-0016e000 rwxp 00162000 00:00 0 0016e000-0023e000 r-xp 00000000 03:06 1887739 /usr/X11R6/lib/libX11.so.6.2 0023e000-00242000 rwxp 000cf000 03:06 1887739 /usr/X11R6/lib/libX11.so.6.2 00242000-00260000 r-xp 00000000 03:06 2777346 /usr/lib/libjpeg.so.62.0.0 00260000-00261000 rwxp 0001d000 03:06 2777346 /usr/lib/libjpeg.so.62.0.0 00261000-00263000 r-xp 00000000 03:06 97835 /usr/lib/R/library/Biobase/libs/Biobase.so 00263000-00264000 rwxp 00001000 03:06 97835 /usr/lib/R/library/Biobase/libs/Biobase.so 00264000-00266000 r-xp 00000000 03:06 1341 /usr/lib/R/library/vsn/libs/vsn.so 00266000-00267000 rwxp 00001000 03:06 1341 /usr/lib/R/library/vsn/libs/vsn.so 00267000-00269000 r-xp 00000000 03:06 65992 /lib/libcom_err.so.2.1 00269000-0026a000 rwxp 00001000 03:06 65992 /lib/libcom_err.so.2.1 00277000-00291000 r-xp 00000000 03:06 65277 /lib/ld-2.3.5.so 00291000-00292000 r-xp 00019000 03:06 65277 /lib/ld-2.3.5.so 00292000-00293000 rwxp 0001a000 03:06 65277 /lib/ld-2.3.5.so 00295000-003b9000 r-xp 00000000 03:06 65279 /lib/libc-2.3.5.so 003b9000-003bb000 r-xp 00124000 03:06 65279 /lib/libc-2.3.5.so 003bb000-003bd000 rwxp 00126000 03:06 65279 /lib/libc-2.3.5.so 003bd000-003bf000 rwxp 003bd000 00:00 0 003c1000-003e3000 r-xp 00000000 03:06 65317 /lib/libm-2.3.5.so 003e3000-003e4000 r-xp 00021000 03:06 65317 /lib/libm-2.3.5.so 003e4000-003e5000 rwxp 00022000 03:06 65317 /lib/libm-2.3.5.so 003e7000-003e9000 r-xp 00000000 03:06 65337 /lib/libdl-2.3.5.so 003e9000-003ea000 r-xp 00001000 03:06 65337 /lib/libdl-2.3.5.so 003ea000-003eb000 rwxp 00002000 03:06 65337 /lib/libdl-2.3.5.so 00402000-00429000 r-xp 00000000 03:06 2777656 /usr/lib/libreadline.so.5.0 00429000-0042d000 rwxp 00027000 03:06 2777656 /usr
Rdbi Rdbi • 858 views
ADD COMMENT

Login before adding your answer.

Traffic: 509 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6